RNAseq Mycobacterium Tuberculosis
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis H37Rv
SUBMITTER: Patricia Del Portillo
PROVIDER: E-GEOD-47863 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We analyzed the genes expressed, or the transcriptome, of bacilli (Mycobacterium tuberculosis) growing in fatty acids as sole carbon source. Using new technologies to massively sequence of RNA molecules we identified a group of genes that provides novel insight regarding the metabolic pathways and transcriptional regulation of latent M. Tuberculosis.
2013-06-13 | GSE47863 | GEO
Project description:Mycobacterium tuberculosis has specialised its metabolism to reside extra- and intra-cellularly in the human host. Nutrient availability and their concentrations can vary dramatically in these niches. Lactate is abundant during infection and it is an important signalling molecule regulating the immune response. In addition, lactate is abundant in blood, epithelial mucosa and a number of other relevant compartments in the host. Interestingly, previous studies have demonstrated that lactate and one of its possible first degradation products, pyruvate, allow superior growth compared to glucose and fatty acids in vitro for M. tuberculosis. Based on this information, we performed a "multi-omics" investigation to study the metabolism of pyruvate and lactate in M. tuberculosis. We employed TraDIS, transcriptomics, proteomics and stable isotopic labelling coupled with mass spectrometry-based metabolomics. Our studies reveal the structure of M. tuberculosis metabolic network associated with catabolism of pyruvate and lactate. Together these findings lead us to reconsider some well-accepted "truths" on carbon metabolism in M. tuberculosis.
2019-11-25 | GSE116859 | GEO
Project description:Bacterial nutrition is a key aspect of host-pathogen interaction and bacteria must adapt to use nutrients available in the host. Lipid droplets-derived fatty acids are considered the major intracellular carbon source for Mycobacterium tuberculosis (Mtb), an intracellular pathogen causing Tuberculosis disease. However, many other (and more soluble) substrates are available in vivo and may represent alternative carbon sources. Lactate and pyruvate are rather abundant in human cells and fluids and represent two possible candidates. In this work, we employed a “multi-omics” approach (Transposon Directed Insertion Site Sequencing (TraDIS), RNA-seq transcriptomics, proteomics and stable isotopic labelling coupled with mass spectrometry-based metabolomics) and classic microbial physiology to study Mtb metabolism of lactate and pyruvate. We discovered that Mtb is well adapted to use lactate and pyruvate as sole carbon sources and that it requires gluconeogenesis, Krebs cycle, GABA shunt, glyoxylate shunt and methylcitrate cycle for their metabolism. These latter are traditionally associated with fatty acid metabolism and unexpectedly, we found that methylcitrate cycle operates in reverse. This latter discovery changes the role of this pathway making it a direct route for the biosynthesis of propionyl-CoA, the essential precursor for the biosynthesis of odd-chain fatty acids, abundantly present in Mtb cell envelope.
2020-05-26 | PXD010726 | Pride
Project description:Amino acids conjugated with even number carbon fatty acids using a coupling of the chloride fatty acids onto amine end of amino acids
2024-04-08 | MSV000094497 | MassIVE
Project description:Whole genome gene expression analysis was examined with Ralstonia eutropha strain H16 cultures grown in PHB production medium (recipe per Peoples and Sinskey, 1989) containing fructose or trioleate as the main carbon source. The goal of this analysis was to determine the identity of the triacylglycerol and fatty acid breakdown genes in R. eutropha strain H16. In the study presented here, triplicates of R. eutropha strain H16 were examined for changes in expression of 6702 genes during growth and PHB production on each carbon source.
2010-08-26 | E-GEOD-21145 | biostudies-arrayexpress
Project description:The capacity of Mycobacterium tuberculosis (Mtb) to sense, respond and adapt to variable and hostile environment within the host, has made it one of the most successful human pathogens. During different stages of infection, the bacillus is surrounding by a plethora of lipid rich molecules and current evidence points out the relevance of fatty acids during the Mtb infectious process. In this study, we have compared the transcriptional response of Mtb to hypoxia in cultures grown in both, a mix of even long-chain fatty acids and dextrose as carbon sources. Using RNA sequencing, we have identified the differential expressed genes in early and late hypoxia defined according to the in vitro Wayne model and compared the results with the exponential phase of growth in both carbon sources. Our results showed that, different to dextrose, the number of genes overexpressed in hypoxia in the lipid medium was quite low in both, early and late hypoxia in all functional categories describes for Mtb. The exception were the transcripts of stable and non-coding RNAs which were more expressed in the fatty acid medium. We found that SigB and SigE were overexpressed in the early phase of hypoxia, confirming their pivotal role in early adaptation to low oxygen concentration independently of the carbon source. A drastic contrast was found with the transcriptional regulatory factors at early hypoxia. Only 2 transcriptional factors were overexpressed in early hypoxia in the lipid medium compared to 37 that were overexpressed in the dextrose medium. Instead of Rv0081, known to be the central regulator of hypoxia in dextrose, Rv2745c, (ClgR), is playing a main role in hypoxia in the fatty acids medium. The low level of genes associated to stress-response, showed by Mtb during their adaptation to hypoxia in fatty acids, suggested that this lipid environment makes hypoxia a less stressful condition for the tubercle bacilli. Therefore, when the bacillus is surviving in that environment, its metabolism seemed to be already adapted to different stresses within the host, including hypoxia. This fact could explain the success of Mtb to establish long-term survival during latent infection.
2018-08-31 | GSE119225 | GEO
Project description:The mycobacterial cell wall is a distinctive thick layer that protects the tubercle bacillus from general antibiotics and the host’s immune system. Mycolic acids, which are long-chain α-alkyl-β-hydroxy fatty acids, are the major constituents of this protective layer, and their synthesis has been shown to be critical for the survival of M. tuberculosis. This model captures the mycolic acid pathway in M. tuberculosis with 197 metabolites participating in 219 reactions catalysed by 28 proteins. The model helps in the rational identification of potential anti-tubercular drug targets.
2023-11-24 | BIOMD0000001046 | BioModels
Project description:This RNA-Seq study of gene expression in M. tuberculosis was done as part of the FLUTE project (NIH grant U19-AI107774, Eric Rubin, program director). There are 3 replicates each for Mtb H37Rv grown under the following conditions: 0.1% butyrate, 0.4% glucose, butyrate+glucose, low iron, acidic conditions, and several RIF-resistant mutants of Beijing strain HN878 with different mutations in RpoB.
2016-03-30 | E-GEOD-67035 | biostudies-arrayexpress
Project description:The Mycobacterium tuberculosis acyl-CoA carboxylases provide the building blocks for de novo fatty acid biosynthesis by fatty acid synthase (FAS) I and for the elongation of FAS I end-products by the FAS II complex to produce meromycolic acids. M. tuberculosis genome contains three biotin carboxylase subunits (AccA1-3) and 6 carboxyltransferase subunits (AccD1-6) of which AccD6 is located in a genetic locus that contains members of the FAS II complex. We found by microarray and quantitative real-time RT-PCR analysis that the transcripts of AccA3, AccD4, AccD5 and AccD6 are expressed at high levels during exponential growth phases of M. tuberculosis in vitro. Keywords: Time course, developmental stages
2006-10-07 | GSE5977 | GEO
Project description:The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status. Hepatic mRNA profiles of Polish Landrace pig breed fed two different diets, were generated by deep sequencing, using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a cotrol. 2 pooled samples each containing RNA extracts from 6 individuals livers were analyzed.
2016-03-15 | E-GEOD-72123 | biostudies-arrayexpress